ABSTRACT: Allogeneic hematopoietic stem cell transplantation is potentially curative therapy for many malignant diseases whose applicability has been impeded by the development of its most serious complication, graft-versus-host disease (GVHD). GVHD results from the damage caused to the host epithelial cell targets by the many immune cells and inflammatory cytokines. While significant progress is being made in understanding the complex role of various immune cells in causing GVHD, little is known about the role played by the target tissues themselves in regulating the severity of disease. Specifically, induction of host intestinal epithelial cell (IEC) apoptosis by the alloreactive donor T cells and inflammatory cytokines causes gastrointestinal (GI) GVHD; however host IEC intrinsic resistance mechanisms to allo-immune T-cell mediated damage, the epigenetic mechanisms that are critical for these resistance mechanisms and its regulation by the tissue resident microflora generated metabolites has never been explored. IEC homeostasis and resistance depends on complex interactions between the metabolic energy substrates (such as short chain fatty acids and amino acid metabolites) and the regulation of transcription and epigenetic chromatin modifications such as histone acetylation. We have demonstrated that epigenetic regulation by systemic administration of histone deacetylase inhibitors (HDACi) regulates experimental GVHD and successfully translated this concept into a proof of principle human trial for prevention of clinical GVHD. Preliminary data generated demonstrate significant alterations in substrates that are derived from microbial metabolites such as essential short chain fatty acids (SCFA) and amino acids metabolites, specifically in butyrate and tryptophan metabolite indole-3-acetaldehyde (I-3-A) levels, in the GI tract (IECs) after allogeneic BMT. Preliminary data also show that (a) butyrate, a known HDACi, enhances histone acetylation, modulates IECs resistance to damage and regulates GVHD (b) expression of aryl hydrocarbon receptor (AhR) (a sensor of tryptophan metabolite indole-3-acetaldehyde) mitigates GVHD severity. But the pathways of sensing and the mechanisms underlying the butyrate and tryptophan metabolite indole-3-acetaldehyde -mediated effects in GVHD remain unknown. Therefore, in this proposal, we will build on these exciting and novel preliminary observations and bring together the diverse fields of microbiota, metabolomics, tissue bioenergetics and epigenetics, to explore the interplay between microbial metabolites and their effects on epigenomic alterations of the IECs in reducing GI GVHD. Specifically, we will test the central premise that regulation of target tissue (IEC) resistance by the endogenous intestinal microbial metabolites butyrate and tryptophan metabolite indole-3-acetaldehyde, alter the acetylation dependent epigenome of IECs and negatively regulates GI GVHD.